angelolab/ark-analysis

Issues

• [v0.8.0] Additional Enhancements

  #1160 opened 2 months ago by srivarra
  0

• Remove Docker

  #1165 opened 2 months ago by srivarra
  0

• Can't run template notebooks "ModuleNotFoundError: No module named 'torch.utils._import_utils'"

  #1150 opened 2 months ago by givison
  1

• `torchdata` import error with M3 Mac

  #1151 opened 2 months ago by dtebaykin
  2

• Remove Spatial Enrichment + Bootstrapping Cython

  #1161 opened 2 months ago by srivarra
  0

• Windows Problem With bash start_docker.sh Command

  #1145 opened 2 months ago by Nicholas-Bartelo
  2

• Use cell table as input for calc_dist_matrix()

  #1154 opened 2 months ago by camisowers
  0

• Update scikit-image / Fiber Segmentation

  #1162 opened 2 months ago by srivarra
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• module 'ark.phenotyping.post_cluster_utils' has no attribute 'generate_new_cluster_resolution'

  #1143 opened 5 months ago by c0urtneyt
  1

• Allow option to turn off numba parallelization

  #1153 opened 3 months ago by alex-l-kong
  0

• `numba` parallelization fault with `relabel_segmentation`

  #1137 opened 7 months ago by alex-l-kong
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• "Unassigned" label not included in "population_cell_mask.csv" for Mantis

  #1141 opened 6 months ago by cliu72
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• OME-TIFF to single channel workflow fails if metadata not contained

  #1155 opened 2 months ago by alex-l-kong
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• AttributeError: module 'ark.utils.plot_utils' has no attribute 'plot_pixel_cell_cluster'

  #1156 opened 2 months ago by smith6jt-cop
  4

• No images found in designated folder for `2_Pixie_Cluster_Pixels.pynb`

  #1148 opened 4 months ago by mezwick
  6

• Error Running example data in templates/2_Pixie_Cluster_Pixels.ipynb

  #1142 opened 4 months ago by mikemcka
  15

• Visualize all markers and cluster names in cell cluster heatmap

  #1146 opened 5 months ago by janinemelsen
  2

• Adjust Github Actions Workflows

  #1138 opened 5 months ago by srivarra
  0

• General signal masking notebook

  #1091 opened 7 months ago by camisowers
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• Error when starting Docker: manifest for angelolab/ark-analysis:v0.7.0 not found

  #1135 opened 7 months ago by fotisn7
  2

• 2_Pixie_Cluster_Pixels notebook error: cluster_pixels() missing 1 required positional argument: 'pixel_pysom'

  #1133 opened 7 months ago by leorrose
  4

• 3_Pixie_Cluster_Cells notebook error. Length mismatch: Expected 5101 rows, received array of length 9931

  #1136 opened 7 months ago by fotisn7
  2

• `numpy.distutils` is deprecated

  #1132 opened 7 months ago by leorrose
  2

• generate neighborhood mask results in string error

  #1129 opened 8 months ago by janinemelsen
  1

• Duplicate FOV name issues with cell table generation

  #1125 opened 8 months ago by camisowers
  0

• Error in `plot_utils.save_colored_masks` and `plot.utils.plot_pixel_cell_cluster`

  #1117 opened 8 months ago by cliu72
  0

• ValueError: pixel_som_clustering.generate_som_avg_files

  #1111 opened 8 months ago by dcomimmo
  18

• Reducing time to merge in merge_masks.py w/i ez_segmenter

  #1119 opened 8 months ago by bryjcannon
  1

• Allow for a subset of FOVs in k-means clustering notebook

  #1122 opened 9 months ago by cliu72
  1

• Generate_cell_table confuses foo1_nuclear and foo10_nuclear

  #1109 opened 9 months ago by g-torr
  1

• ValueError: Lists pixel som weights columns and pixel data columns ordered differently

  #1120 opened 9 months ago by janinemelsen
  1

• Pixel Subset in Pixie

  #1118 opened 9 months ago by matthew-lee1
  5

• FOV names not parsed correctly when running example dataset in `1_Segment_Image_Data.ipynb`

  #1096 opened 9 months ago by cliu72
  1

• marker_quantification.process_lists() returning inappropriate mask_types

  #1103 opened 9 months ago by bryjcannon
  0

• Empty composites, masks in ez_segmenter notebook.

  #1100 opened 9 months ago by bryjcannon
  0

• Error downloading example dataset

  #1116 opened 9 months ago by cliu72
  2

• Error in `create_mantis_dir` in cell clustering notebook if running `generate_and_save_cell_cluster_masks` multiple times

  #1099 opened 9 months ago by cliu72
  2

• Even when setting `nuclear_counts = False`, nuclear masks are being quantified in `marker_quantification.generate_cell_table`

  #1097 opened 9 months ago by cliu72
  0

• Order column pixel_pysom differs from feather file

  #1115 opened 9 months ago by janinemelsen
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• Example Dataset is causing tests to fail

  #1113 opened 9 months ago by srivarra
  0

• AnnData spatial analysis part 1

  #1105 opened a year ago by camisowers
  4

• Remove pixels that were not assigned to cells

  #1108 opened 10 months ago by janinemelsen
  2

• Cell clustering unable to parse updated cell table format from `ez_seg` update

  #1106 opened 10 months ago by alex-l-kong
  2

• Cannot run through example dataset in `3_Pixie_Cluster_Cells.ipynb`

  #1098 opened a year ago by cliu72
  1

• `IntCastingNaNError` in 3_Pixie_Cluster_Cells notebook

  #1094 opened a year ago by sarafiller
  1

• Incorrect cell cluster mapping in mantis

  #1082 opened a year ago by camisowers
  2

• Error with Pixie

  #1085 opened a year ago by Nitya20001
  1

• ConnectionResetError when using deepcell_service_utils.create_deepcell_output

  #1088 opened a year ago by coding0lion
  0

• Pixel clustering with Pixie - error

  #1084 opened a year ago by Nitya20001
  0

• 2_Pixie_Cluster_Pixel.ipynb not creating pixel_meta_cluster_mapping.csv

  #1086 opened a year ago by milesbailey121
  0